Conductive atomic force microscopy (CAFM) has been widely used for electrical characterization of thin dielectrics by applying a gentle contact force that ensures a good electrical contact without inducing additional high‐pressure related phenomena (e.g., flexoelectricity, local heat, scratching). Recently, the CAFM has been used to obtain 3D electrical images of thin dielectrics by etching their surface. However, the effect of the high contact forces/pressures applied during the etching on the electrical properties of the materials has never been considered. By collecting cross‐sectional transmission electron microscopy images at the etched regions, it is shown here that the etching process can modify the morphology of Al2O3 thin films (producing phase change, generation of defects, and metal penetration). It is also observed that this technique severely modifies the electrical properties of pSi and TiO2 wafers during the etching, and several behaviors ignored in previous studies, including i) observation of high currents in the absence of bias, ii) instabilities of etching rate, and iii) degradation of CAFM tips, are reported. Overall, this work should contribute to understand better the limitations of this technique and disseminate it among those applications in which it can be really useful.